VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Jul 12 2007 - 21:56:32 CDT

Hi Shyamala,
this sounds like it might be a topology file issue. If you can send me
one of your top files off-list I can have a look. If you're actually
using x-plor format topologies (not charmm), that's probably the
problem, as psfgen doesn't read these.

Best,
Peter

shyamala wrote:
>
> Hi all,
>
> I am fairly new to VMD and NAMD. I am trying to immerse a protein
> dimer in a box of water.
>
> I am using the following script to accomplish the task.
>
> package require psfgen
> package require solvate
>
> # X-PLOR topology files
> topology ./topallhdg.inp
> topology ./toptip3p.inp
>
> pdbalias atom ILE CD1 CD
> pdbalias residue HOH TIP3
> pdbalias atom HOH O OH2
>
> set prot "1hbv"
> mol load pdb ${prot}.pdb
>
> set all [atomselect top "all"]
> set hivp [atomselect top "protein"]
>
> set chainA [atomselect top "chain A"]
> set chainB [atomselect top "chain B"]
> set xtalH2O [atomselect top "water and resid 501"]
> set ligand [atomselect top "resname GAN"]
>
> $chainA writepdb ${prot}_A.pdb
> $chainB writepdb ${prot}_B.pdb
> $xtalH2O writepdb ${prot}_H2O.pdb
> $ligand writepdb ${prot}_lig.pdb
>
> resetpsf
>
> segment A {
> first PROP
> pdb ${prot}_A.pdb
> }
> coordpdb ${prot}_A.pdb A
>
> segment B {
> first PROP
> pdb ${prot}_B.pdb
> }
> coordpdb ${prot}_B.pdb B
>
> segment H {pdb ${prot}_H2O.pdb}
> coordpdb ${prot}_H2O.pdb H
>
> guesscoord
>
> writepdb ${prot}_dry.pdb
> writepsf x-plor ${prot}_dry.psf
>
> solvate ${prot}_dry.psf ${prot}_dry.pdb -t 5 -o ${prot}_wb
>
> set all [atomselect top "all"]
>
> echo "Min and max box coordinates:"
> measure minmax $all
> echo "Center of box:"
> measure center $all
>
> exit
>
> when I run the script in vmd, I get the following error:
> building segment A
> setting patch for first residue to PROP
> reading residues from pdb file 1hbv_A.pdb
> extracted 99 residues from pdb file
> Info: generating structure...
> unknown atom type +CA
> add atom failed in patch PROP
> ERROR: failed on end of segment
>
> I am not really sure what this means. Both chains A and B of the
> protein dimer have a N term Proline (residue 1). I am using xplor
> topology files.
>
> I would really appreciate it if someone could give some ideas about
> what is going wrong.
>
> Thanks,
>
> Shyamala Iyer
> University of Washington, Seattle
>